Ligand profile

ZINC103619636

Virtual-screening candidate from ZINC.

Bound to: VK055_3627 — 4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

Via homolog UniProt O52327 Formula C₁₂H₁₆N₆O₆
Tanimoto 0.61
Mol. weight 340.30 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC103619636
UniProt (similar protein)
O52327
Tanimoto
0.611
Target protein
VK055_3627

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 340.30 Da
LogP (Crippen) 1.54
H-bond donors 0
H-bond acceptors 8
TPSA 176.42 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 24
Fraction sp³ C 0.75
Formula C₁₂H₁₆N₆O₆

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 176.4
  • −1 ≤ LogP ≤ 5 1.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 340.3
  • LogP ≤ 5 1.54
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 176.4
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)O[C@H]1[C@H](N=[N+]=[N-])C[C@H](N=[N+]=[N-])[C@@H](OC(C)=O)[C@@H]1OC(C)=O
InChI 
InChI=1S/C12H16N6O6/c1-5(19)22-10-8(15-17-13)4-9(16-18-14)11(23-6(2)20)12(10)24-7(3)21/h8-12H,4H2,1-3H3/t8-,9+,10+,11-,12-
InChIKey 
SQKWPVVWVBKSIG-CSPFCNMYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
CHEMBL255766
Homolog
O52327

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3627.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)